lmer-class               package:lme4               R Documentation

_M_i_x_e_d _m_o_d_e_l _r_e_p_r_e_s_e_n_t_a_t_i_o_n_s

_D_e_s_c_r_i_p_t_i_o_n:

     The 'mer' class is mixed-effects representation using a blocked,
     sparse, symmetric, column-oriented matrix and dense matrices. The
     'lmer' class extends 'mer' to represent a fitted linear
     mixed-effects model.  The 'glmer' class extends 'lmer' to
     represent a fitted generalized linear mixed-effects model.  The
     'summary.lmer' class represents summaries of these objects.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form 'new("lmer", ...)' or,
     more commonly, via the 'lmer' function or by applying the
     'summary' generic to a 'glmer' or 'lmer' object.

_S_l_o_t_s:

     '_f_l_i_s_t': The list of (possibly permuted) grouping factors for the
          random effects.

     '_p_e_r_m': A list of permutation vectors applied to the grouping
          factors.

     '_P_a_r_e_n_t': The extended parent array for the diagonal elements of
          'L'.

     '_b_V_a_r': A list of the diagonal inner blocks (upper triangles only)
          of the positive-definite matrices on the diagonal of the
          inverse of Z'Z+W.

     '_L': The blocked sparse representation of the unit lower
          triangular matrix in the LDL' factorization of Z'Z+W.

     '_Z_Z_p_O': Object of class '"list"' ~~ 

     '_O_m_e_g_a': A list of numeric matrices providing the components of
          symmetric, positive-definite matrix Omega.  Only the upper
          triangle of each component is used and stored.

     '_D': A list of the diagonal factors (upper triangle) in the LDL'
          decomposition of Z'Z+W.

     '_R_E_M_L': A '"logical"' indicator of whether the REML criterion is
          being used to determine parameter estimates.

     '_R_X_X': A matrix which is the (augmented) RXX component or the
          corresponding component from the inverse of Z'Z+W

     '_R_Z_X': A matrix which is the (augmented) RZX component or the
          corresponding component from the inverse of Z'Z+W

     '_Z_t_Z': The blocks in the blocked sparse symmetric representation
          of the original Z'Z matrix

     '_X_t_X': The original X'X matrix

     '_Z_t_X': The original Z'X matrix

     '_c_n_a_m_e_s': Column names of the model matrices.

     '_d_e_v_C_o_m_p': Numeric vector of length 4 giving the components used
          to calculate the deviance. This slot's contents are current
          if 'status$factored' is 'TRUE'.

     '_d_e_v_i_a_n_c_e': Numeric vector of length 2 containing the deviance
          corresponding to the maximum likelihood (ML) and REML
          criteria.  This slot's contents are current if
          'status$factored' is 'TRUE'.

     '_n_c': Integer vector of the number of columns in (augmented) model
          matrices and the number of observations in the model frame.

     '_G_p': Integer vector of 0-based row numbers of the 'ZtX' and 'RZX'
          matrices where new groups begin. groups of rows in  .in -5

     '_s_t_a_t_u_s': Logical vector of length 2 indicating if the object has
          been factored and if the factorization has been inverted.

     '_c_a_l_l': A copy of the matched call to the function that created
          the object.

     '_u_s_e_S_c_a_l_e': logical indicator of the use of the scale factor when
          calculating variance-covariance objects.  Only present in the
          'summary.lmer' class.

     '_s_h_o_w_C_o_r_r_e_l_a_t_i_o_n': Logical indicator of whether to display the
          correlation of the fixed-effects estimates when showing the
          object. Only present in the 'summary.lmer' class.

_M_e_t_h_o_d_s:

     _c_o_e_f 'signature(object = "lmer")': Extract the parameters that
          determine the Omega matrices.  The optional logical argument
          'unconstr' determines the constrained or unconstrained
          parameterization.

     _c_o_e_f<- 'signature(object = "lmer", value = "numeric")': Assign the
          parameters that determine the Omega matrices.  The optional
          logical argument 'unconstr' determines the constrained or
          unconstrained parameterization. 

     _c_o_e_r_c_e 'signature(from = "lmer", to = "dtTMatrix")': Ensure that
          the 'lmer' object has been factored but not inverted and
          extract the unit lower triangular matrix L from the LDL
          decomposition of crossprod(Z)+Omega.

     _c_o_e_r_c_e 'signature(from = "lmer", to = "dsTMatrix")': Ensure that
          the 'lmer' object has been factored but not inverted and
          extract the symmetric matrix crossprod(Z)+Omega.

     _s_o_l_v_e 'signature(a = "lmer", b = "missing")': Invert the
          decomposed matrices.

